Stochastic Simulation of Biomolecular Networks in Dynamic Environments.

ABSTRACT: Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several or

SUBMITTER: Voliotis M 

PROVIDER: S-EPMC4889045 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature